Table 1 Comparison between methods. (A) APC comparisons are shown below the main diagonal whereas MAD comparisons are shown above the main diagonal. (B) APC comparisons between methods based on all CpGs, or after restricting to those located close to sequence variants or those located within dark regions as indicated

(A) Consistency between methods

Mean absolute difference (MAD)

OxBS

ONT Nanopolish

ONT Guppy R9.4

ONT Guppy R10.4

PacBio

APC

OxBS

-

0.05933

0.05730

0.04772

0.05691

ONT Nanopolish

0.9460

-

0.05040

0.04888

0.05207

ONT guppy R9.4

0.9594

0.9653

-

0.04655

0.04608

ONT guppy R10.4

0.9647

0.9637

0.9817

-

0.04363

PacBio

0.9563

0.9571

0.9705

0.9785

-

(B) Consistency between methods in sequencing context

APC

NP vs. Guppy R9.4

NP vs. Guppy R10.4

NP vs. PacBio

NP vs. oxBS

Guppy R9.4 vs. Guppy R10.4

Guppy R9.4 vs. PacBio

Guppy R9.4 vs. oxBS

Guppy R10.4 vs. oxBS

Guppy R10.4 vs. PacBio

PacBio vs. oxBS

All CpGs

0.965

0.963

0.957

0.959

0.982

0.971

0.972

0.978

0.979

0.970

CpGs near sequence variants

0.930

0.921

0.913

0.922

0.973

0.957

0.940

0.934

0.962

0.929

CpGs within dark regions

0.841

0.845

0.841

0.698

0.906

0.873

0.716

0.736

0.876

0.691